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The main game is largely similar to previous installments in the series, in that the player controls a Mini Toy trying to reach the end of the stage. By scanning a compatible Mario series-related amiibo, the player can receive the corresponding toy to play as, while the Mini Spek is received by scanning any other amiibo. Each Mini Toy (with the exception of the Mini Spek) has a special ability that allows it to clear stages easier. At the end of each stage, players are given a score based on their performance, and by clearing it with a high enough score, the player earns a Gold Trophy for that stage.

Within certain main stages are amiibo Doors, which can only be accessed by the corresponding character on the door and unlock special stages themed around that character. Some stages also feature amiibo Tokens, which don't work in any other game and can only be obtained by using the abilities of the amiibo on the token.

Ledge Grab: If Mini Diddy Kong walks off a cliff, he will grab on to the ledge, instead of falling, and pull himself back up to safety. This won't work with ledges that are the same height as the fall.

In addition to the main stages in the game, there are also worlds themed around each character toy that can be unlocked by clearing certain stages via an amiibo door, which can only be accessed by using the amiibo that corresponds with the character's icon shown on it.[5]

Balloon Float Castle: Mini Peach's world whose mechanic are balloons that fly in the direction of the arrow once Mini Peach grabs onto one. The music that plays is the Peach's castle theme from Super Mario 64.[7]

Moonlight Mansion: Mini Luigi's world, based on the Luigi's Mansion games. Its main mechanic is candles that can be removed and placed in different spots to stun the Mini Boos and reveal hidden blocks that can be passed through without a torch, but cannot be passed through with one. The music that plays is a cover of the mansion theme of Luigi's Mansion.

Air Tumble Rumble: Mini Bowser Jr.'s world in which the main gimmick is fans that push the player across gaps, which alternate between turning on and off by tapping them. The music that plays is a cover of Bowser Jr.'s battle theme in New Super Mario Bros. Wii.[8]

Super Mario 64: Mini Peach's levels are based on her castle from this game, and use a remix of "Inside the Castle Walls" as the background music. In addition to this, Mini Bowser's levels use a remix of his battle theme from this game as background music. Mini Mario's ability originated in this game. The Warp pipe sound is the same as this game

Luigi's Mansion: Mini Luigi's levels use a remix of this game's main theme as background music.

New Super Mario Bros. Wii: Mini Mario's levels are based on this game, with the background resembling world 1 of said game. Mini Bowser Jr.'s levels are based on the game's airship levels as well, and use a remix of Bowser Jr.'s battle theme as background music.

Super Mario Galaxy: Mini Rosalina's levels are based on this game, and are set in the Comet Observatory. The background music is a remix of the observatory and Luma's theme music.